CA3030038A1 - Methods for fragmentome profiling of cell-free nucleic acids - Google Patents
Methods for fragmentome profiling of cell-free nucleic acids Download PDFInfo
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- CA3030038A1 CA3030038A1 CA3030038A CA3030038A CA3030038A1 CA 3030038 A1 CA3030038 A1 CA 3030038A1 CA 3030038 A CA3030038 A CA 3030038A CA 3030038 A CA3030038 A CA 3030038A CA 3030038 A1 CA3030038 A1 CA 3030038A1
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- cell
- dna
- dna fragments
- fragments
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
- C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
- G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B20/10—Ploidy or copy number detection
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
- G16B30/10—Sequence alignment; Homology search
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/154—Methylation markers
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
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- Life Sciences & Earth Sciences (AREA)
- Health & Medical Sciences (AREA)
- Physics & Mathematics (AREA)
- Engineering & Computer Science (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Medical Informatics (AREA)
- Biotechnology (AREA)
- Biophysics (AREA)
- General Health & Medical Sciences (AREA)
- Chemical & Material Sciences (AREA)
- Bioinformatics & Computational Biology (AREA)
- Evolutionary Biology (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Theoretical Computer Science (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Analytical Chemistry (AREA)
- Genetics & Genomics (AREA)
- Molecular Biology (AREA)
- Computer Vision & Pattern Recognition (AREA)
- Evolutionary Computation (AREA)
- Software Systems (AREA)
- Public Health (AREA)
- Epidemiology (AREA)
- Databases & Information Systems (AREA)
- Data Mining & Analysis (AREA)
- Bioethics (AREA)
- Artificial Intelligence (AREA)
- Organic Chemistry (AREA)
- Pathology (AREA)
- Zoology (AREA)
- Immunology (AREA)
- Wood Science & Technology (AREA)
- Microbiology (AREA)
- General Engineering & Computer Science (AREA)
- Hospice & Palliative Care (AREA)
- Biochemistry (AREA)
- Oncology (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Apparatus Associated With Microorganisms And Enzymes (AREA)
- Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
Applications Claiming Priority (9)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201662359151P | 2016-07-06 | 2016-07-06 | |
| US62/359,151 | 2016-07-06 | ||
| US201662420167P | 2016-11-10 | 2016-11-10 | |
| US62/420,167 | 2016-11-10 | ||
| US201662437172P | 2016-12-21 | 2016-12-21 | |
| US62/437,172 | 2016-12-21 | ||
| US201762489399P | 2017-04-24 | 2017-04-24 | |
| US62/489,399 | 2017-04-24 | ||
| PCT/US2017/040986 WO2018009723A1 (en) | 2016-07-06 | 2017-07-06 | Methods for fragmentome profiling of cell-free nucleic acids |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| CA3030038A1 true CA3030038A1 (en) | 2018-01-11 |
Family
ID=60913158
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA3030038A Pending CA3030038A1 (en) | 2016-07-06 | 2017-07-06 | Methods for fragmentome profiling of cell-free nucleic acids |
Country Status (11)
| Country | Link |
|---|---|
| EP (2) | EP3481966B1 (enExample) |
| JP (3) | JP7448310B2 (enExample) |
| KR (1) | KR102610098B1 (enExample) |
| CN (1) | CN109689891B (enExample) |
| AU (1) | AU2017292854B2 (enExample) |
| BR (1) | BR112019000296A2 (enExample) |
| CA (1) | CA3030038A1 (enExample) |
| ES (1) | ES2967443T3 (enExample) |
| MX (1) | MX2019000037A (enExample) |
| SG (1) | SG11201811556RA (enExample) |
| WO (1) | WO2018009723A1 (enExample) |
Cited By (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| EP3884087A1 (en) | 2018-11-21 | 2021-09-29 | Karius Inc. | Detection and prediction of infectious disease |
| US12320036B2 (en) | 2018-11-21 | 2025-06-03 | Karius, Inc. | Direct-to-library methods, systems, and compositions |
| US12595509B2 (en) | 2016-03-25 | 2026-04-07 | Karius, Inc. | Synthetic nucleic acid spike-ins |
Families Citing this family (129)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US11111544B2 (en) | 2005-07-29 | 2021-09-07 | Natera, Inc. | System and method for cleaning noisy genetic data and determining chromosome copy number |
| US9424392B2 (en) | 2005-11-26 | 2016-08-23 | Natera, Inc. | System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals |
| US11111543B2 (en) | 2005-07-29 | 2021-09-07 | Natera, Inc. | System and method for cleaning noisy genetic data and determining chromosome copy number |
| US10316362B2 (en) | 2010-05-18 | 2019-06-11 | Natera, Inc. | Methods for simultaneous amplification of target loci |
| US11332793B2 (en) | 2010-05-18 | 2022-05-17 | Natera, Inc. | Methods for simultaneous amplification of target loci |
| US11339429B2 (en) | 2010-05-18 | 2022-05-24 | Natera, Inc. | Methods for non-invasive prenatal ploidy calling |
| US11408031B2 (en) | 2010-05-18 | 2022-08-09 | Natera, Inc. | Methods for non-invasive prenatal paternity testing |
| US11332785B2 (en) | 2010-05-18 | 2022-05-17 | Natera, Inc. | Methods for non-invasive prenatal ploidy calling |
| US11326208B2 (en) | 2010-05-18 | 2022-05-10 | Natera, Inc. | Methods for nested PCR amplification of cell-free DNA |
| US9677118B2 (en) | 2014-04-21 | 2017-06-13 | Natera, Inc. | Methods for simultaneous amplification of target loci |
| US20190010543A1 (en) | 2010-05-18 | 2019-01-10 | Natera, Inc. | Methods for simultaneous amplification of target loci |
| US12152275B2 (en) | 2010-05-18 | 2024-11-26 | Natera, Inc. | Methods for non-invasive prenatal ploidy calling |
| US11939634B2 (en) | 2010-05-18 | 2024-03-26 | Natera, Inc. | Methods for simultaneous amplification of target loci |
| US8825412B2 (en) | 2010-05-18 | 2014-09-02 | Natera, Inc. | Methods for non-invasive prenatal ploidy calling |
| US11322224B2 (en) | 2010-05-18 | 2022-05-03 | Natera, Inc. | Methods for non-invasive prenatal ploidy calling |
| US12221653B2 (en) | 2010-05-18 | 2025-02-11 | Natera, Inc. | Methods for simultaneous amplification of target loci |
| EP2656263B1 (en) | 2010-12-22 | 2019-11-06 | Natera, Inc. | Methods for non-invasive prenatal paternity testing |
| JP6153874B2 (ja) | 2011-02-09 | 2017-06-28 | ナテラ， インコーポレイテッド | 非侵襲的出生前倍数性呼び出しのための方法 |
| AU2012242847B2 (en) | 2011-04-15 | 2017-01-19 | The Johns Hopkins University | Safe sequencing system |
| US20140100126A1 (en) | 2012-08-17 | 2014-04-10 | Natera, Inc. | Method for Non-Invasive Prenatal Testing Using Parental Mosaicism Data |
| ES2701742T3 (es) | 2012-10-29 | 2019-02-25 | Univ Johns Hopkins | Prueba de Papanicolaou para cánceres de ovario y de endometrio |
| CN113774132A (zh) | 2014-04-21 | 2021-12-10 | 纳特拉公司 | 检测染色体片段中的突变和倍性 |
| US20180173846A1 (en) | 2014-06-05 | 2018-06-21 | Natera, Inc. | Systems and Methods for Detection of Aneuploidy |
| DK3294906T3 (en) | 2015-05-11 | 2024-08-05 | Natera Inc | Methods for determining ploidy |
| US10453556B2 (en) | 2015-07-23 | 2019-10-22 | The Chinese University Of Hong Kong | Analysis of fragmentation patterns of cell-free DNA |
| WO2017027653A1 (en) | 2015-08-11 | 2017-02-16 | The Johns Hopkins University | Assaying ovarian cyst fluid |
| DK3443119T3 (da) | 2016-04-15 | 2022-05-23 | Natera Inc | Fremgangsmåde til bestemmelse af lunge cancer |
| WO2018067517A1 (en) | 2016-10-04 | 2018-04-12 | Natera, Inc. | Methods for characterizing copy number variation using proximity-litigation sequencing |
| GB201618485D0 (en) | 2016-11-02 | 2016-12-14 | Ucl Business Plc | Method of detecting tumour recurrence |
| US10011870B2 (en) | 2016-12-07 | 2018-07-03 | Natera, Inc. | Compositions and methods for identifying nucleic acid molecules |
| WO2018119452A2 (en) | 2016-12-22 | 2018-06-28 | Guardant Health, Inc. | Methods and systems for analyzing nucleic acid molecules |
| ES2990117T3 (es) | 2017-01-25 | 2024-11-28 | Univ Hong Kong Chinese | Aplicaciones de diagnóstico que utilizan fragmentos de ácido nucleico |
| WO2019016353A1 (en) * | 2017-07-21 | 2019-01-24 | F. Hoffmann-La Roche Ag | CLASSIFICATION OF SOMATIC MUTATIONS FROM A HETEROGENEOUS SAMPLE |
| CN120400338A (zh) | 2017-08-07 | 2025-08-01 | 约翰斯霍普金斯大学 | 用于评估和治疗癌症的方法和材料 |
| WO2019060716A1 (en) | 2017-09-25 | 2019-03-28 | Freenome Holdings, Inc. | SAMPLE EXTRACTION METHODS AND SYSTEMS |
| WO2019118926A1 (en) | 2017-12-14 | 2019-06-20 | Tai Diagnostics, Inc. | Assessing graft suitability for transplantation |
| EP3743518A4 (en) * | 2018-01-24 | 2021-09-29 | Freenome Holdings, Inc. | METHODS AND SYSTEMS FOR DETECTING ANOMALY IN PATTERNS OF NUCLEIC ACIDS |
| IL321982A (en) * | 2018-02-27 | 2025-09-01 | Univ Cornell | Systems and methods for detecting residual disease |
| JP2021519607A (ja) | 2018-02-27 | 2021-08-12 | コーネル・ユニバーシティーＣｏｒｎｅｌｌ Ｕｎｉｖｅｒｓｉｔｙ | ゲノムワイド統合による循環腫瘍ｄｎａの超音波感受性検出 |
| WO2019173552A1 (en) | 2018-03-08 | 2019-09-12 | St. John's University | Circulating serum cell-free dna biomarkers and methods |
| WO2019178289A1 (en) | 2018-03-13 | 2019-09-19 | Grail, Inc. | Method and system for selecting, managing, and analyzing data of high dimensionality |
| WO2019178563A1 (en) * | 2018-03-15 | 2019-09-19 | The Board Of Trustees Of Leland Stanford Junior University | Methods using nucleic acid signals for revealing biological attributes |
| WO2019200404A2 (en) * | 2018-04-13 | 2019-10-17 | Grail, Inc. | Multi-assay prediction model for cancer detection |
| CA3095056A1 (en) * | 2018-04-13 | 2019-10-17 | Freenome Holdings, Inc. | Machine learning implementation for multi-analyte assay of biological samples |
| DK3781714T3 (da) | 2018-04-14 | 2026-03-30 | Natera Inc | Fremgangsmåder til cancerpåvisning og -overvågning ved personlig påvisning af cirkulerende tumor-dna |
| CN112888459B (zh) | 2018-06-01 | 2023-05-23 | 格里尔公司 | 卷积神经网络系统及数据分类方法 |
| WO2020006369A1 (en) * | 2018-06-29 | 2020-01-02 | Guardant Health, Inc. | Methods and systems for analysis of ctcf binding regions in cell-free dna |
| US12234509B2 (en) | 2018-07-03 | 2025-02-25 | Natera, Inc. | Methods for detection of donor-derived cell-free DNA |
| JP7637615B2 (ja) * | 2018-09-04 | 2025-02-28 | ガーダント ヘルス， インコーポレイテッド | 無細胞核酸試料におけるアレル不均衡を検出するための方法およびシステム |
| EP3815005A4 (en) * | 2018-10-08 | 2022-03-30 | Freenome Holdings, Inc. | Transcription factor profiling |
| GB201818159D0 (en) * | 2018-11-07 | 2018-12-19 | Cancer Research Tech Ltd | Enhanced detection of target dna by fragment size analysis |
| US10468141B1 (en) * | 2018-11-28 | 2019-11-05 | Asia Genomics Pte. Ltd. | Ancestry-specific genetic risk scores |
| US11581062B2 (en) | 2018-12-10 | 2023-02-14 | Grail, Llc | Systems and methods for classifying patients with respect to multiple cancer classes |
| TW202536188A (zh) * | 2018-12-19 | 2025-09-16 | 香港中文大學 | 游離dna末端特徵 |
| WO2020127629A1 (en) * | 2018-12-21 | 2020-06-25 | F. Hoffmann-La Roche Ag | Identification of global sequence features in whole genome sequence data from circulating nucelic acid |
| WO2020132499A2 (en) * | 2018-12-21 | 2020-06-25 | Grail, Inc. | Systems and methods for using fragment lengths as a predictor of cancer |
| WO2020150258A1 (en) * | 2019-01-15 | 2020-07-23 | Luminist, Inc. | Methods and systems for detecting liver disease |
| KR102916051B1 (ko) * | 2019-01-24 | 2026-01-21 | 일루미나, 인코포레이티드 | 장기 건강 및 질환을 모니터링하기 위한 방법 및 시스템 |
| CA3126428A1 (en) | 2019-01-31 | 2020-08-06 | Guardant Health, Inc. | Compositions and methods for isolating cell-free dna |
| CA3130203A1 (en) | 2019-02-12 | 2020-08-20 | Tempus Labs, Inc. | Detection of human leukocyte antigen loss of heterozygosity |
| US11475978B2 (en) | 2019-02-12 | 2022-10-18 | Tempus Labs, Inc. | Detection of human leukocyte antigen loss of heterozygosity |
| WO2020176659A1 (en) * | 2019-02-27 | 2020-09-03 | Guardant Health, Inc. | Methods and systems for determining the cellular origin of cell-free dna |
| US20220154249A1 (en) * | 2019-04-15 | 2022-05-19 | Natera, Inc. | Improved liquid biopsy using size selection |
| US12497662B2 (en) | 2019-04-16 | 2025-12-16 | Grail, Inc. | Systems and methods for tumor fraction estimation from small variants |
| US11869661B2 (en) | 2019-05-22 | 2024-01-09 | Grail, Llc | Systems and methods for determining whether a subject has a cancer condition using transfer learning |
| US11939636B2 (en) | 2019-05-31 | 2024-03-26 | Guardant Health, Inc. | Methods and systems for improving patient monitoring after surgery |
| EP3980559A1 (en) | 2019-06-06 | 2022-04-13 | Natera, Inc. | Methods for detecting immune cell dna and monitoring immune system |
| EP3997242B1 (en) * | 2019-07-09 | 2026-04-08 | The Translational Genomics Research Institute | Methods of detecting disease and treatment response in cfdna |
| US20220301654A1 (en) * | 2019-08-28 | 2022-09-22 | Grail, Llc | Systems and methods for predicting and monitoring treatment response from cell-free nucleic acids |
| CN110706749B (zh) * | 2019-09-10 | 2022-06-10 | 至本医疗科技（上海）有限公司 | 一种基于组织器官分化层次关系的癌症类型预测系统和方法 |
| CA3151538A1 (en) | 2019-09-30 | 2021-04-08 | Stefanie Ann Ward Mortimer | Compositions and methods for analyzing cell-free dna in methylation partitioning assays |
| EP4715839A2 (en) | 2019-10-11 | 2026-03-25 | Guardant Health, Inc. | Use of cell free bacterial nucleic acids for detection of cancer |
| CN114746560A (zh) | 2019-11-26 | 2022-07-12 | 夸登特健康公司 | 改进甲基化多核苷酸结合的方法、组合物和系统 |
| KR102586651B1 (ko) * | 2019-11-29 | 2023-10-11 | 주식회사 지씨지놈 | 인공지능 기반 염색체 이상 검출 방법 |
| CN115151657A (zh) * | 2019-12-20 | 2022-10-04 | 安可济控股有限公司 | 用于疾病检测的方法和系统 |
| WO2021130356A1 (en) * | 2019-12-24 | 2021-07-01 | Vib Vzw | Disease detection in liquid biopsies |
| IL295297A (en) | 2020-02-14 | 2022-10-01 | Univ Johns Hopkins | Methods and materials for assessing nucleic acids |
| AU2021227920A1 (en) * | 2020-02-28 | 2022-09-08 | Grail, Llc | Systems and methods for calling variants using methylation sequencing data |
| CA3177127A1 (en) | 2020-04-30 | 2021-11-04 | Guardant Health, Inc. | Methods for sequence determination using partitioned nucleic acids |
| IL298458A (en) * | 2020-05-22 | 2023-01-01 | Aqtual Inc | Methods for characterizing cell-free nucleic acid fragments |
| EP4179111B1 (en) | 2020-07-10 | 2024-04-03 | Guardant Health, Inc. | Methods of detecting genomic rearrangements using cell free nucleic acids |
| WO2023282916A1 (en) | 2021-07-09 | 2023-01-12 | Guardant Health, Inc. | Methods of detecting genomic rearrangements using cell free nucleic acids |
| WO2022026761A1 (en) | 2020-07-30 | 2022-02-03 | Guardant Health, Inc. | Methods for isolating cell-free dna |
| CN116157868A (zh) * | 2020-08-18 | 2023-05-23 | 德尔菲诊断公司 | 用于游离dna片段大小密度以评估癌症的方法和系统 |
| WO2022046947A1 (en) | 2020-08-25 | 2022-03-03 | Guardant Health, Inc. | Methods and systems for predicting an origin of a variant |
| EP4214329A4 (en) * | 2020-09-17 | 2024-12-04 | The Regents of the University of Colorado, a body corporate | Signatures in cell-free dna to detect disease, track treatment response, and inform treatment decisions |
| WO2022073012A1 (en) | 2020-09-30 | 2022-04-07 | Guardant Health, Inc. | Compositions and methods for analyzing dna using partitioning and a methylation-dependent nuclease |
| WO2022087309A1 (en) | 2020-10-23 | 2022-04-28 | Guardant Health, Inc. | Compositions and methods for analyzing dna using partitioning and base conversion |
| CA3199829A1 (en) | 2020-11-30 | 2022-06-02 | Guardant Health, Inc. | Compositions and methods for enriching methylated polynucleotides |
| CN114634982A (zh) * | 2020-12-15 | 2022-06-17 | 广州市基准医疗有限责任公司 | 一种检测多核苷酸变异的方法 |
| EP4015650A1 (en) * | 2020-12-18 | 2022-06-22 | Nipd Genetics Biotech Limited | Methods for classifying a sample into clinically relevant categories |
| WO2022140629A1 (en) | 2020-12-23 | 2022-06-30 | Guardant Health, Inc. | Methods and systems for analyzing methylated polynucleotides |
| EP4729633A2 (en) | 2021-02-12 | 2026-04-22 | Guardant Health, Inc. | Methods for detecting nucleic acid variants |
| EP4314329A1 (en) | 2021-03-25 | 2024-02-07 | Guardant Health, Inc. | Methods and compositions for quantifying immune cell dna |
| EP4320277A4 (en) * | 2021-04-08 | 2025-03-05 | Delfi Diagnostics, Inc. | CANCER DETECTION METHOD USING GENOME-WIDE CELL-FREE DNA FRAGMENTATION PROFILES |
| WO2022248844A1 (en) * | 2021-05-24 | 2022-12-01 | University Of Essex Enterprises Limited | Method and system for identifying genomic regions with condition sensitive occupancy/positioning of nucleosomes and/or chromatin |
| KR102927037B1 (ko) * | 2021-05-28 | 2026-02-13 | 주식회사 지씨지놈 | 조직 특이적 조절 지역의 무세포 dna 분포를 이용한 인공지능 기반 암 조기진단 방법 |
| CN113838533B (zh) * | 2021-08-17 | 2024-03-12 | 福建和瑞基因科技有限公司 | 一种癌症检测模型及其构建方法和试剂盒 |
| EP4433611A4 (en) * | 2021-11-17 | 2025-10-08 | Univ Leland Stanford Junior | SYSTEMS AND METHODS FOR GENE EXPRESSION AND TISSUE OF ORIGIN INFERENCE FROM CIRCULATING FREE DNA |
| KR102884871B1 (ko) * | 2022-01-26 | 2025-11-11 | 권창혁 | 암 판별 장치 및 암 판별 방법 |
| CA3245713A1 (en) * | 2022-03-17 | 2023-09-21 | Delfi Diagnostics, Inc. | CANCER SURVEILLANCE METHOD USING FRAGMENTATION PROFILES |
| EP4504971A1 (en) | 2022-04-07 | 2025-02-12 | Guardant Health, Inc. | Detecting the presence of a tumor based on methylation status of cell-free nucleic acid molecules |
| EP4532762A1 (en) * | 2022-06-02 | 2025-04-09 | The Board Of Trustees Of The Leland Stanford Junior University | Single molecule sequencing and methylation profiling of cell-free dna |
| EP4547857A1 (en) | 2022-06-30 | 2025-05-07 | Guardant Health, Inc. | Enrichment of aberrantly methylated dna |
| US20240043935A1 (en) * | 2022-07-29 | 2024-02-08 | Centre For Novostics Limited | Epigenetics analysis of cell-free dna |
| WO2024073508A2 (en) | 2022-09-27 | 2024-04-04 | Guardant Health, Inc. | Methods and compositions for quantifying immune cell dna |
| CN115295074B (zh) * | 2022-10-08 | 2022-12-16 | 南京世和基因生物技术股份有限公司 | 基因标志物在恶性肺结节筛查中的应用、筛查模型的构建方法和检测装置 |
| WO2024112643A1 (en) * | 2022-11-21 | 2024-05-30 | Foundation Medicine, Inc. | Fragmentomics based identification of tumor-specific copy number alteration states in liquid biopsy |
| WO2024138180A2 (en) | 2022-12-22 | 2024-06-27 | Guardant Health, Inc. | Integrated targeted and whole genome somatic and dna methylation sequencing workflows |
| EP4638781A2 (en) | 2022-12-22 | 2025-10-29 | Guardant Health, Inc. | Methods involving methylation preserving amplification with error correction |
| EP4705522A1 (en) | 2023-05-05 | 2026-03-11 | Guardant Health, Inc. | Cell-free dna blood-based test for cancer screening |
| CN116665784B (zh) * | 2023-05-31 | 2025-12-30 | 华中农业大学 | 基于cfDNA全基因组测序数据识别染色质开放区域的方法、癌症预测模型及系统 |
| WO2025019370A1 (en) * | 2023-07-14 | 2025-01-23 | Natera, Inc. | Methods for assaying circulating tumor dna |
| WO2025029475A1 (en) | 2023-07-28 | 2025-02-06 | Guardant Health, Inc. | Methods to enrich nucleotide variants by negative selection |
| WO2025038399A1 (en) | 2023-08-11 | 2025-02-20 | Guardant Health, Inc. | Methylated enrichment methods for single-molecule genetic and epigenetic sequencing |
| CN117230165A (zh) * | 2023-09-01 | 2023-12-15 | 深圳湾实验室 | 一种无创产前检测胎儿染色体拷贝数异常的优化方法 |
| WO2025064706A1 (en) | 2023-09-19 | 2025-03-27 | Guardant Health, Inc. | Detecting the presence of a tumor based on methylation status of cell-free nucleic acid molecules |
| WO2025076452A1 (en) | 2023-10-06 | 2025-04-10 | Guardant Health, Inc. | Detecting tumor-related information based on methylation status of cell-free nucleic acid molecules |
| WO2025207817A1 (en) | 2024-03-26 | 2025-10-02 | Guardant Health, Inc. | Method of determining the likelihood of a disease by combining biomarkers and imaging |
| WO2025208044A1 (en) | 2024-03-28 | 2025-10-02 | Guardant Health, Inc. | Methods for cancer detection using molecular patterns |
| WO2025205006A1 (ja) * | 2024-03-29 | 2025-10-02 | ソニーグループ株式会社 | 分析方法、クロマチン状態を分類する方法、がん検査方法、分析システム、がん又は微小残存病変の検査システムおよび分析キット |
| WO2025235889A1 (en) | 2024-05-10 | 2025-11-13 | Guardant Health, Inc. | Methods involving multiplexed pooled pcr |
| WO2025250544A1 (en) | 2024-05-31 | 2025-12-04 | Guardant Health, Inc. | Methods for analyzing chromatin architecture in tissue to boost detection of cancer associated signals in cell-free dna |
| WO2026043718A1 (en) | 2024-08-21 | 2026-02-26 | Guardant Health, Inc. | Methods to monitor patients treated with a cancer vaccine |
| WO2026073140A1 (en) | 2024-09-27 | 2026-04-02 | Guardant Health, Inc. | Framework to identify genomic regions indicative of one or more biological conditions |
| WO2026076332A1 (en) | 2024-10-03 | 2026-04-09 | Guardant Health, Inc. | Methods involving multi-modal tumor variant identification and tracking of tumor molecules |
| WO2026090570A1 (en) | 2024-10-24 | 2026-04-30 | Guardant Health, Inc. | Detecting the presence of a biological condition based on a nucleic acid sample data analysis |
| CN119905148B (zh) * | 2024-12-30 | 2026-02-06 | 西藏自治区农牧科学院水产科学研究所 | 一种核间等位基因表达分析方法、装置及存储介质 |
| CN120334449B (zh) * | 2025-06-20 | 2025-09-05 | 陕西右任故里茯砖茶股份有限公司 | 基于液相色谱的茯砖茶中金花菌发酵检测方法 |
Family Cites Families (21)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| BRPI0920069A8 (pt) | 2008-10-30 | 2017-10-03 | Centre De Rech Public De La Sante | Biomarcadores |
| CN101901345B (zh) * | 2009-05-27 | 2013-02-27 | 复旦大学 | 一种差异蛋白质组学的分类方法 |
| US11322224B2 (en) * | 2010-05-18 | 2022-05-03 | Natera, Inc. | Methods for non-invasive prenatal ploidy calling |
| EP2426217A1 (en) * | 2010-09-03 | 2012-03-07 | Centre National de la Recherche Scientifique (CNRS) | Analytical methods for cell free nucleic acids and applications |
| CA2840418C (en) * | 2011-07-26 | 2019-10-29 | Verinata Health, Inc. | Method for determining the presence or absence of different aneuploidies in a sample |
| US9367663B2 (en) * | 2011-10-06 | 2016-06-14 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| EP3922731A3 (en) | 2011-10-06 | 2022-01-05 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| CA2866587C (en) | 2012-02-16 | 2022-07-26 | Oxford Nanopore Technologies Limited | Analysis of measurements of a polymer |
| AU2013232123B2 (en) * | 2012-03-13 | 2014-10-30 | The Chinese University Of Hong Kong | Methods for analyzing massively parallel sequencing data for noninvasive prenatal diagnosis |
| CN108485940B (zh) * | 2012-04-12 | 2022-01-28 | 维里纳塔健康公司 | 拷贝数变异的检测和分类 |
| US10497461B2 (en) | 2012-06-22 | 2019-12-03 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| DE202013012824U1 (de) * | 2012-09-04 | 2020-03-10 | Guardant Health, Inc. | Systeme zum Erfassen von seltenen Mutationen und einer Kopienzahlvariation |
| US20160040229A1 (en) | 2013-08-16 | 2016-02-11 | Guardant Health, Inc. | Systems and methods to detect rare mutations and copy number variation |
| US20130309666A1 (en) * | 2013-01-25 | 2013-11-21 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| CN114574581A (zh) * | 2013-03-15 | 2022-06-03 | 夸登特健康公司 | 检测稀有突变和拷贝数变异的系统和方法 |
| EP3011052B1 (en) * | 2013-06-17 | 2019-05-22 | Verinata Health, Inc | Method for determining copy number variations in sex chromosomes |
| US9499870B2 (en) * | 2013-09-27 | 2016-11-22 | Natera, Inc. | Cell free DNA diagnostic testing standards |
| ES2660989T3 (es) | 2013-12-28 | 2018-03-27 | Guardant Health, Inc. | Métodos y sistemas para detectar variantes genéticas |
| JP6659672B2 (ja) * | 2014-05-30 | 2020-03-04 | ベリナタ ヘルス インコーポレイテッド | 胎児染色体部分異数性およびコピー数変動の検出 |
| CA2956208C (en) * | 2014-07-25 | 2025-07-08 | University Of Washington | METHODS FOR DETERMINING TISSUES AND/OR CELL TYPES RENDERING CELL-FREE DNA AND RELATED METHODS FOR DETERMINING A DISEASE OR DISORDER |
| AU2015360298B2 (en) * | 2014-12-12 | 2018-06-07 | Verinata Health, Inc. | Using cell-free DNA fragment size to determine copy number variations |
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Cited By (5)
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|---|---|---|---|---|
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| EP3884087A1 (en) | 2018-11-21 | 2021-09-29 | Karius Inc. | Detection and prediction of infectious disease |
| EP3884087A4 (en) * | 2018-11-21 | 2022-09-07 | Karius Inc. | DETECTION AND PREDICTION OF INFECTIOUS DISEASES |
| US12320036B2 (en) | 2018-11-21 | 2025-06-03 | Karius, Inc. | Direct-to-library methods, systems, and compositions |
| US12601089B2 (en) | 2018-11-21 | 2026-04-14 | Karius, Inc. | Direct-to-library methods, systems, and compositions |
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| EP4322168A2 (en) | 2024-02-14 |
| JP2022025101A (ja) | 2022-02-09 |
| BR112019000296A2 (pt) | 2019-04-16 |
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